Yeast resequencing data updated

Image from http://www.bath.ac.uk/bio-sci/wheals2.htmThe Saccharomyces Genome Resequencing Project has completed ” ABI sequencing of 32 S. cerevisiae strains and 27 S. paradoxus strains to a depth of between 1x and 3x”. This is in collaboration with Ed Louis’ group who have been working on number of really interesting fungal biology and evolutionary questions.

So 59 strains across two species from this project, plus deep-coverage (or finished) genomes from 3 strains. The lab “mouse” S288C that is well-annotated and the 1st eukaryotic genome to be sequenced. There is the”wild” vineyard strain RM11-1A. And a clinical isolate from an AIDS patient YJM789. The S. paradoxus strain sequenced by the Whitehead a few years ago also provides a scaffold for the strain sequencing.

This dataset along with another 100 strains proposed by Justin Fay and Leonid Kruglyak make for a really interesting time in population and association studies in fungi. In many cases we don’t know that much about the ecological history of strains (unlike what has been done in the Neurospora such as the collections of David Perkins). Paul Sniegowski has collected several populations of Saccharomyces from the environment and investigated reproductive and population parameters among these. Many of his soil and tree isolates are part of the resequencing and expression studies.

3 thoughts on “Yeast resequencing data updated”

  1. How good are the assemblies for identifying anything other than SNPs? Can they use any of the assemblies to look at structural polymorphisms?

  2. The Sanger (Centre) light-draft assemblies (0.5-2x) are only really good enough for polymorphism detection I would surmise. Indels can be believed here since it is Sanger (as in the method) sequencing better than if it had been 454 sequencing. They have some positive controls in terms of some known rearrangements that we can see if they are detectable, but I agree that we probably won’t be able to talk about large scale rearrangements from this data alone. I think that Ed Louis’s group is working to get telomere’s properly assembled for many of the strains. Since that is where a lot of the horizontal transfer action is happening.

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